vegan: ordiarrows – R documentation

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ordiarrows

Add Arrows and Line Segments to Ordination Diagrams

Description

Functions to add arrows, line segments, regular grids of points. The ordination diagrams can be produced by vegan plot.cca, plot.decorana or ordiplot.

Usage

ordiarrows(ord, groups, levels, replicates, order.by, display = "sites",
         col = 1, show.groups, startmark, label = FALSE, length = 0.1, ...)
ordisegments(ord, groups, levels, replicates, order.by, display = "sites",
         col = 1, show.groups, label = FALSE, ...)
ordigrid(ord, levels, replicates, display = "sites",  lty = c(1,1), 
         col = c(1,1), lwd = c(1,1), ...)

Arguments

`ord`	An ordination object or an `ordiplot` object.
`groups`	Factor giving the groups for which the graphical item is drawn.
`levels, replicates`	Alternatively, regular groups can be defined with arguments `levels` and `replicates`, where `levels` gives the number of groups, and `replicates` the number of successive items at the same group.
`order.by`	Order points by increasing order of this variable within `groups`. Reverse sign of the variable for decreasing ordering.
`display`	Item to displayed.
`show.groups`	Show only given groups. This can be a vector, or `TRUE` if you want to show items for which condition is `TRUE`. This argument makes it possible to use different colours and line types for groups. The default is to show all groups.
`label`	Label the `groups` by their names. In `ordiellipse`, `ordihull` and `ordispider` the the group name is in the centroid of the object, in `ordiarrows` in the start of the arrow, and in `ordisegments` at both ends. `ordiellipse` and `ordihull` use standard `text`, and others use `ordilabel`.
`startmark`	plotting character used to mark the first item. The default is to use no mark, and for instance, `startmark = 1` will draw a circle. For other plotting characters, see `pch` in `points`.
`col`	Colour of lines, `label` borders and `startmark` in `ordiarrows` and `ordisegments`. This can be a vector recycled for `groups`. In `ordigrid` it can be a vector of length 2 used for `levels` and `replicates`.
`length`	Length of edges of the arrow head (in inches).
`lty, lwd`	Line type, line width used for `level`s and `replicate`s in `ordigrid`.
`...`	Parameters passed to graphical functions such as `lines`, `segments`, `arrows`, or to `scores` to select axes and scaling etc.

Details

Function ordiarrows draws arrows and ordisegments draws line segments between successive items in the groups. Function ordigrid draws line segments both within the groups and for the corresponding items among the groups.

Note

These functions add graphical items to ordination graph: You must draw a graph first.

Author(s)

Jari Oksanen

Examples

example(pyrifos)
mod <- rda(pyrifos)
plot(mod, type = "n")
## Annual succession by ditches, colour by dose
ordiarrows(mod, ditch, label = TRUE, col = as.numeric(dose))
legend("topright", levels(dose), lty=1, col=1:5, title="Dose")
## Show only control and highest Pyrifos treatment
plot(mod, type = "n")
ordiarrows(mod, ditch, label = TRUE, 
   show.groups = c("2", "3", "5", "11"))
ordiarrows(mod, ditch, label = TRUE, show = c("6", "9"),
   col = 2)
legend("topright", c("Control", "Pyrifos 44"), lty = 1, col = c(1,2))

vegan

Community Ecology Package

v2.5-7

GPL-2

Authors

Jari Oksanen, F. Guillaume Blanchet, Michael Friendly, Roeland Kindt, Pierre Legendre, Dan McGlinn, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Eduard Szoecs, Helene Wagner

Initial release